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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ), 'gf_id' => 'HOM05D001345', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001345' ), 'data_identifier' => 'HOM05D001345', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001345', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '467', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p00270' => 'bna', 'A03p27380' => 'bna', 'A06p17150' => 'bna', 'A07p42360' => 'bna', 'A07p42640' => 'bna', 'A08p29080' => 'bna', 'A09p58180' => 'bna', 'Aa31LG10G9840' => 'aar', 'Aa31LG4G6780' => 'aar', 'Aa31LG4G7080' => 'aar', 'Aa31LG6G16110' => 'aar', 'Aa31LG7G15020' => 'aar', 'Aa31LG7G5230' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.2003' => 'aag', 'Actinidia00545' => 'ach', 'Actinidia03436' => 'ach', 'Actinidia29503' => 'ach', 'Actinidia29504' => 'ach', 'Actinidia37898' => 'ach', 'Ah.01g019150' => 'amhyb', 'Ah.05g169250' => 'amhyb', 'Ah.11g042670' => 'amhyb', 'AL1G34130' => 'aly', 'AL2G36850' => 'aly', 'AL2G37190' => 'aly', 'AL4G10700' => 'aly', 'AL734U10010' => 'aly', 'AL7G11090' => 'aly', 'Aqoxy5G00906' => 'aox', 'Aqoxy6G00268' => 'aox', 'Aqoxy6G01187' => 'aox', 'Aqoxy6G01189' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6M2MGC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73E5NM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J5ATDZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JU3PXC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZV34CK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZYC0YM' => 'arhy', 'AT1G21080' => 'ath', 'AT1G76700' => 'ath', 'AT1G77020' => 'ath', 'AT2G21510' => 'ath', 'AT4G39150' => 'ath', 'ATR0585G018' => 'atr', 'ATR0605G175' => 'atr', 'ATR0820G020' => 'atr', 'Atru.chr13.1649' => 'acertr', 'Atru.chr13.9' => 'acertr', 'Atru.chr5.3077' => 'acertr', 'Atru.chr5.3079' => 'acertr', 'AUR62007670' => 'cqu', 'AUR62011289' => 'cqu', 'AUR62013464' => 'cqu', 'AUR62016770' => 'cqu', 'AUR62035196' => 'cqu', 'AUR62042528' => 'cqu', 'AUR62042529' => 'cqu', 'BcaB01g02968' => 'bca', 'BcaB03g12835' => 'bca', 'BcaB03g14282' => 'bca', 'BcaB07g32101' => 'bca', 'BcaC01g04864' => 'bca', 'BcaC05g26016' => 'bca', 'BcaC06g34888' => 'bca', 'BcaC07g37536' => 'bca', 'BcaC07g39076' => 'bca', 'BcaC07g41152' => 'bca', 'BcaC08g47180' => 'bca', 'BcaC08g47204' => 'bca', 'BcaC08g47222' => 'bca', 'BcaNung01276' => 'bca', 'BolC1t00044H' => 'bol', 'BolC3t15628H' => 'bol', 'BolC5t30680H' => 'bol', 'BolC6t38281H' => 'bol', 'BolC6t40118H' => 'bol', 'BolC6t40145H' => 'bol', 'BolC7t42747H' => 'bol', 'BolC8t49689H' => 'bol', 'BolC8t49692H' => 'bol', 'BolC8t51706H' => 'bol', 'BraA01t00034Z' => 'bra', 'BraA03t11949Z' => 'bra', 'BraA06t24818Z' => 'bra', 'BraA07t31763Z' => 'bra', 'BraA07t31786Z' => 'bra', 'BraA08t34843Z' => 'bra', 'BraA09t41207Z' => 'bra', 'C01p00380' => 'bna', 'C03p32990' => 'bna', 'C04p16990' => 'bna', 'C05p19800' => 'bna', 'C06p31530' => 'bna', 'C06p50920' => 'bna', 'C06p51230' => 'bna', 'C07p22480' => 'bna', 'C08p20600' => 'bna', 'C08p41450' => 'bna', 'CAN.G1544.4' => 'can', 'CAN.G208.46' => 'can', 'CAN.G46.4' => 'can', 'CANSAT11G1464' => 'cansat', 'CANSAT21G0481' => 'cansat', 'CANSAT21G1833' => 'cansat', 'CANSAT25G0067' => 'cansat', 'CARHR021530' => 'chi', 'CARHR053310' => 'chi', 'CARHR070240' => 'chi', 'CARHR070550' => 'chi', 'CARHR110810' => 'chi', 'CARHR112430' => 'chi', 'CARHR247600' => 'chi', 'Carub.0001s2054' => 'cru', 'Carub.0002s2360' => 'cru', 'Carub.0002s2394' => 'cru', 'Carub.0004s0055' => 'cru', 'Carub.0007s0103' => 'cru', 'Ca_12654_v3' => 'car', 'Ca_12671_v3' => 'car', 'Ca_23907_v3' => 'car', 'Ca_24328_v3' => 'car', 'CBR_g50001' => 'cbr', 'Cc00_g15100' => 'ccan', 'Cc10_g00030' => 'ccan', 'Cc10_g13210' => 'ccan', 'Cc10_g13220' => 'ccan', 'CDE04G1846' => 'cde', 'CDE06G1351' => 'cde', 'CDE07G0387' => 'cde', 'Cfa005047' => 'cfa', 'Cfa014180' => 'cfa', 'Cfa018392' => 'cfa', 'Cfa027247' => 'cfa', 'Ciclev10001330m.g' => 'ccl', 'Ciclev10003893m.g' => 'ccl', 'Ciclev10028792m.g' => 'ccl', 'CiPaw.06G133100' => 'cil', 'CiPaw.07G128600' => 'cil', 'CiPaw.07G128800' => 'cil', 'CiPaw.08G079800' => 'cil', 'CiPaw.15G023900' => 'cil', 'ClCG03G011430' => 'cla', 'ClCG07G003380' => 'cla', 'ClCG08G006310' => 'cla', 'ClCG11G004180' => 'cla', 'ClCG11G019240' => 'cla', 'COL.COLO4_16222' => 'col', 'COL.COLO4_25980' => 'col', 'COL.COLO4_35491' => 'col', 'Cpa.g.c42818' => 'cpa', 'Cpa.g.sc106.7' => 'cpa', 'Cpa.g.sc26.75' => 'cpa', 'Cpa.g.sc36.85' => 'cpa', 'Cpa.g.sc753.1' => 'cpa', 'Cre06.g260350' => 'cre', 'CsaV3_2G014990' => 'csa', 'CsaV3_4G037840' => 'csa', 'CsaV3_6G031130' => 'csa', 'CSS0006725' => 'camsi', 'CSS0011724' => 'camsi', 'CSS0021414' => 'camsi', 'CSS0025560' => 'camsi', 'CSS0040281' => 'camsi', 'DCAR_003658' => 'dca', 'DCAR_009843' => 'dca', 'DCAR_013345' => 'dca', 'DCAR_014396' => 'dca', 'DCAR_028969' => 'dca', 'Dinv05525' => 'din', 'Dinv25779' => 'din', 'Dinv42041' => 'din', 'Duzib041G0769' => 'dzi', 'Duzib052G0329' => 'dzi', 'Duzib066G0006' => 'dzi', 'Duzib128G0510' => 'dzi', 'Duzib132G0046' => 'dzi', 'Duzib248G0621' => 'dzi', 'ECA233G0672' => 'eca', 'ECA236G2451' => 'eca', 'ECA240G2586' => 'eca', 'ECA246G2590' => 'eca', 'EL10Ac1g01413' => 'bvu', 'EL10Ac1g01839' => 'bvu', 'EL10Ac9g21694' => 'bvu', 'Eucgr.F01962' => 'egr', 'Eucgr.F01963' => 'egr', 'Eucgr.F04280' => 'egr', 'Eucgr.G01646' => 'egr', 'Eucgr.G02150' => 'egr', 'Eucgr.G02152' => 'egr', 'Eucgr.L02883' => 'egr', 'FAN04G0765' => 'fan', 'FAN08G2804' => 'fan', 'FAN13G1933' => 'fan', 'FAN15G1446' => 'fan', 'FAN15G2961' => 'fan', 'FAN18G2316' => 'fan', 'FAN20G1019' => 'fan', 'FAN20G1738' => 'fan', 'FAN24G0743' => 'fan', 'FAN24G1795' => 'fan', 'FAN24G3451' => 'fan', 'FAN24G3514' => 'fan', 'FAN27G0695' => 'fan', 'FAN27G1769' => 'fan', 'FAN27G3045' => 'fan', 'FvH4_2g09550' => 'fve', 'FvH4_2g09560' => 'fve', 'FvH4_2g15170' => 'fve', 'FvH4_5g26910' => 'fve', 'Glyma.01G245600' => 'gma', 'Glyma.01G245700' => 'gma', 'Glyma.11G178505' => 'gma', 'Glyma.12G235500' => 'gma', 'Glyma.13G036700' => 'gma', 'Glyma.13G200800' => 'gma', 'Glyma.14G118300' => 'gma', 'Gohir.A02G109400' => 'ghi', 'Gohir.A04G124400' => 'ghi', 'Gohir.A06G180700' => 'ghi', 'Gohir.A12G042600' => 'ghi', 'Gohir.A13G009100' => 'ghi', 'Gohir.A13G032700' => 'ghi', 'Gohir.D03G062200' => 'ghi', 'Gohir.D04G166500' => 'ghi', 'Gohir.D06G187500' => 'ghi', 'Gohir.D12G029700' => 'ghi', 'Gohir.D13G009800' => 'ghi', 'Gohir.D13G030833' => 'ghi', 'Gorai.008G030600' => 'gra', 'Gorai.010G219800' => 'gra', 'Gorai.012G154900' => 'gra', 'Gorai.013G010500' => 'gra', 'Gorai.013G035100' => 'gra', 'Gorai.013G107100' => 'gra', 'GSVIVG01009982001' => 'vvi', 'GSVIVG01013476001' => 'vvi', 'GSVIVG01023820001' => 'vvi', 'HanXRQChr03g0069281' => 'han', 'HanXRQChr05g0160461' => 'han', 'HanXRQChr07g0204421' => 'han', 'HanXRQChr08g0216981' => 'han', 'HanXRQChr08g0232411' => 'han', 'HanXRQChr10g0310141' => 'han', 'Haze_02334' => 'cav', 'Haze_17676' => 'cav', 'Haze_22905' => 'cav', 'Hma1.2p1_0066F.1_g036160' => 'hma', 'Hma1.2p1_0851F.1_g228440' => 'hma', 'HPP92_008534' => 'vpl', 'HPP92_018869' => 'vpl', 'HPP92_018870' => 'vpl', 'HPP92_018871' => 'vpl', 'Hund05059' => 'sun', 'Hund06254' => 'sun', 'Hund17377' => 'sun', 'Lalb_Chr03g0032891' => 'lal', 'Lalb_Chr04g0263611' => 'lal', 'Lalb_Chr16g0376201' => 'lal', 'Lalb_Chr16g0376211' => 'lal', 'Lalb_Chr25g0281581' => 'lal', 'Lj1g0010770' => 'lja', 'Lj1g0020049' => 'lja', 'Lj1g0022033' => 'lja', 'Lj3g0001593' => 'lja', 'Lj4A815G23' => 'lonja', 'Lj4A815G26' => 'lonja', 'Lj4A815T25' => 'lonja', 'Lj5A194G78' => 'lonja', 'Lj9A377T86' => 'lonja', 'Lj9C377T5' => 'lonja', 'Lsat_1_v5_gn_3_821' => 'lsa', 'Lsat_1_v5_gn_6_97261' => 'lsa', 'Lsat_1_v5_gn_7_91540' => 'lsa', 'Lsat_1_v5_gn_8_25721' => 'lsa', 'Lsat_1_v5_gn_9_108061' => 'lsa', 'Manes.02G172700' => 'mes', 'Manes.04G087332' => 'mes', 'Manes.05G113900' => 'mes', 'Manes.18G085200' => 'mes', 'Mapoly0130s0038' => 'mpo', 'MBI01_g32837_MAGBIO' => 'mbi', 'MBI01_g32840_MAGBIO' => 'mbi', 'MBI06_g27444_MAGBIO' => 'mbi', 'MBI10_g00751_MAGBIO' => 'mbi', 'MBI16_g36845_MAGBIO' => 'mbi', 'MCO16G446' => 'mco', 'MD05G1010600' => 'mdo', 'MD05G1061900' => 'mdo', 'MD10G1009300' => 'mdo', 'MD10G1069700' => 'mdo', 'MD12G1067400' => 'mdo', 'MD14G1067500' => 'mdo', 'Medtr1g029460' => 'mtr', 'Medtr1g029470' => 'mtr', 'Medtr5g004570' => 'mtr', 'Medtr5g004600' => 'mtr', 'Medtr8g037810' => 'mtr', 'MELO3C008428.2' => 'cme', 'MELO3C017077.2' => 'cme', 'MELO3C023319.2' => 'cme', 'Migut.B00212' => 'egut', 'Migut.C00327' => 'egut', 'Migut.N03004' => 'egut', 'Migut.N03250' => 'egut', 'MSTRG.20064' => 'ama', 'MSTRG.22065' => 'ama', 'MSTRG.24534' => 'ama', 'MSTRG.24886' => 'ama', 'Nitab4.5_0000174g0100' => 'nta', 'Nitab4.5_0001309g0100' => 'nta', 'Nitab4.5_0003234g0140' => 'nta', 'Nitab4.5_0003423g0090' => 'nta', 'Nitab4.5_0003622g0060' => 'nta', 'Nitab4.5_0026658g0010' => 'nta', 'Nn1g05812' => 'nnu', 'Nn5g28516' => 'nnu', 'Nn5g29704' => 'nnu', 'Nn6g31512' => 'nnu', 'Oeu000726.1' => 'oeu', 'Oeu014731.2' => 'oeu', 'Oeu020738.1' => 'oeu', 'Oeu046148.1' => 'oeu', 'Os01g0702450' => 'osa', 'Os02g0555700' => 'osa', 'Os05g0543700' => 'osa', 'Os08g0522600' => 'osa', 'Os09g0493800' => 'osa', 'Peaxi162Scf00016g00430' => 'pax', 'Peaxi162Scf00064g01527' => 'pax', 'Peaxi162Scf00066g01630' => 'pax', 'PGR042G3765' => 'pgr', 'PGR044G1341' => 'pgr', 'PGR083G2256' => 'pgr', 'PGSC0003DMG400024837' => 'stu', 'PGSC0003DMG400030947' => 'stu', 'PGSC0003DMG401029307' => 'stu', 'Phvul.001G064900' => 'pvu', 'Phvul.002G055050' => 'pvu', 'Phvul.007G115900' => 'pvu', 'Phvul.011G210000' => 'pvu', 'Potri.002G000300' => 'ptr', 'Potri.002G074600' => 'ptr', 'Potri.004G158300' => 'ptr', 'Potri.005G185800' => 'ptr', 'Potri.005G260400' => 'ptr', 'Potri.009G119800' => 'ptr', 'Pp3c15_8150' => 'ppa', 'Pp3c23_15320' => 'ppa', 'Pp3c23_15410' => 'ppa', 'Pp3c24_13630' => 'ppa', 'Pp3c24_14260' => 'ppa', 'Pp3c9_13020' => 'ppa', 'PRCOL_00000771' => 'pco', 'PRCOL_00004100' => 'pco', 'PRCOL_00005323' => 'pco', 'Prupe.7G066900' => 'ppe', 'Prupe.8G013200' => 'ppe', 'Prupe.8G091300' => 'ppe', 'Prupe.8G091400' => 'ppe', 'Psat0s4560g0040' => 'psa', 'Psat4g148000' => 'psa', 'Psat6g039760' => 'psa', 'Psat6g071400' => 'psa', 'PSO017G7280' => 'pso', 'PSO170G3355' => 'pso', 'PSO170G6651' => 'pso', 'PSO528G0227' => 'pso', 'PSO541G1540' => 'pso', 'PSO675G5750' => 'pso', 'QL02p016607' => 'qlo', 'QL09p029487' => 'qlo', 'QL10p058583' => 'qlo', 'QL10p059290' => 'qlo', 'QL11p045194' => 'qlo', 'RcHm_v2.0_Chr6g0265841' => 'rch', 'RcHm_v2.0_Chr6g0265851' => 'rch', 'RcHm_v2.0_Chr6g0277831' => 'rch', 'RcHm_v2.0_Chr7g0217951' => 'rch', 'Rhsim04G0034100' => 'rsi', 'Rhsim07G0258500' => 'rsi', 'Rhsim07G0258600' => 'rsi', 'Rhsim11G0075100' => 'rsi', 'Rhsim11G0180200' => 'rsi', 'RhsimUnG0100600' => 'rsi', 'Sabra02G0000500' => 'sbr', 'Sabra02G0000600' => 'sbr', 'Sabra02G0058100' => 'sbr', 'Sabra05G0142000' => 'sbr', 'Sabra05G0201100' => 'sbr', 'SalBow6G1283' => 'sbo', 'SalBow6G4056' => 'sbo', 'SalBow7G3454' => 'sbo', 'Sc02g0004590' => 'sci', 'Sc02g0009390' => 'sci', 'Sc08g0000630' => 'sci', 'Sc14g0002040' => 'sci', 'Sc18g0005070' => 'sci', 'Sc18g0005090' => 'sci', 'Sed0000381' => 'sed', 'Sed0009748' => 'sed', 'Sed0012695' => 'sed', 'Sed0023133' => 'sed', 'SEGI_38964' => 'sgi', 'SEGI_39118' => 'sgi', 'SGA_v2.0_scaffold19G08689' => 'sas', 'SGA_v2.0_scaffold25G11029' => 'sas', 'SGA_v2.0_scaffold58G20505' => 'sas', 'SHI05558' => 'shi', 'SHI05559' => 'shi', 'SHI05560' => 'shi', 'SMO351G0018' => 'smo', 'Solyc01g109890.3' => 'sly', 'Solyc04g063390.2' => 'sly', 'Solyc12g095800.2' => 'sly', 'Sopen01g052080' => 'spe', 'Sopen04g026310' => 'spe', 'Sopen12g031700' => 'spe', 'Sp1g18750' => 'spa', 'Sp4g00670' => 'spa', 'Sp5g31850' => 'spa', 'Sp5g32180' => 'spa', 'Sp7g36670' => 'spa', 'TAR376G0216' => 'tar', 'TAR376G0400' => 'tar', 'TAR376G1043' => 'tar', 'TAR376G1117' => 'tar', 'TAR378G0003' => 'tar', 'TAR381G1421' => 'tar', 'TAR628G1692' => 'tar', 'THA.LOC104812029' => 'tha', 'THA.LOC104812063' => 'tha', 'Thecc.02G080800' => 'tca', 'Thecc.08G096300' => 'tca', 'Thecc.08G138600' => 'tca', 'Thhalv10000200m.g' => 'esa', 'Thhalv10000223m.g' => 'esa', 'Thhalv10007857m.g' => 'esa', 'Thhalv10018664m.g' => 'esa', 'Thhalv10018713m.g' => 'esa', 'Thhalv10019530m.g' => 'esa', 'Thhalv10025633m.g' => 'esa', 'TPR.G1713' => 'tpr', 'TPR.G1891' => 'tpr', 'TPR.G21619' => 'tpr', 'TPR.G33309' => 'tpr', 'TWI12G0120' => 'twi', 'TWI32G0339' => 'twi', 'TWI34G0262' => 'twi', 'TWI56G0941' => 'twi', 'TWI75G1428' => 'twi', 'TWI79G0450' => 'twi', 'unitig_8.g3411' => 'ugi', 'vmacro00879' => 'vma', 'vmacro00880' => 'vma', 'vmacro02080' => 'vma', 'vmacro04435' => 'vma', 'vmacro04436' => 'vma', 'VMungo1127G1699' => 'vmu', 'VMungo1215G0679' => 'vmu', 'VMungo1215G1159' => 'vmu', 'Zm00001eb035420' => 'zma', 'Zm00001eb243690' => 'zma', 'Zm00001eb294570' => 'zma', 'Zm00001eb317080' => 'zma', 'Zm00001eb342590' => 'zma', 'Zm00001eb361030' => 'zma' ) $gf_id = 'HOM05D001345' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001345' ) $data_identifier = 'HOM05D001345' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 6, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 4, 'cqu' => (int) 7, 'bca' => (int) 14, 'bol' => (int) 10, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 4, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 5, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 7, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 4, 'oeu' => (int) 4, 'osa' => (int) 5, 'pax' => (int) 3, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 3, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 6, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 6, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 3, 'shi' => (int) 3, 'smo' => (int) 1, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 7, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb361030' $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